Merge branch 'main' into release

client/src/app/components/events/event-feed/event-feed.component.ts

@@ -18,6 +18,7 @@ import { Observable } from 'rxjs';
 import { map } from 'rxjs/operators';
 import { TagLinkableOrganization } from "@app/components/organizations/organization-tag/organization-tag.component";
 import { TagLinkableUser } from "@app/components/users/user-tag/user-tag.component";
+import { environment } from "environments/environment";
 
 interface SelectableAction { id: EventAction }
 
@@ -65,7 +66,11 @@ export class CvcEventFeedComponent implements OnInit {
       showFilters: this.showFilters
     }
 
-    this.queryRef = this.gql.watch(this.initialQueryVars, {});
+    if(environment.production) {
+      this.queryRef = this.gql.watch(this.initialQueryVars, {pollInterval: 30000});
+    } else {
+      this.queryRef = this.gql.watch(this.initialQueryVars);
+    }
     this.results$ = this.queryRef.valueChanges;
 
     this.pageInfo$ = this.results$.pipe(

client/src/app/components/flags/flaggable/flaggable.module.ts

@@ -6,11 +6,13 @@ import { NzToolTipModule } from 'ng-zorro-antd/tooltip';
 import { NzTypographyModule } from 'ng-zorro-antd/typography';
 import { NzBadgeModule } from 'ng-zorro-antd/badge';
 import { NzIconModule } from 'ng-zorro-antd/icon';
+import { RouterModule } from '@angular/router';
 
 @NgModule({
   declarations: [CvcFlaggableComponent, CvcFlaggableOptionsDirective],
   imports: [
     CommonModule,
+    RouterModule,
     NzIconModule,
     NzBadgeModule,
     NzToolTipModule,

client/src/app/components/layout/viewer-button/viewer-button.component.html

@@ -17,7 +17,6 @@
         nzTheme="outline"></i>
     </button>
     <nz-badge [nzCount]="unreadCount"
-      nzShowZero
       [nzOverflowCount]="999"
       [nzStyle]="{ backgroundColor: '#096dd9', color: '#fff1f0',  boxShadow: '0 0 0 1px #1890ff inset' }"
       *nzSpaceItem>

client/src/app/components/layout/viewer-button/viewer-button.component.ts

@@ -4,6 +4,7 @@ import { Viewer, ViewerService } from '@app/core/services/viewer/viewer.service'
 import { Maybe, ViewerNotificationCountGQL } from '@app/generated/civic.apollo';
 import { startWith, map } from 'rxjs/operators';
 import { NzModalRef, NzModalService } from 'ng-zorro-antd/modal';
+import { environment } from 'environments/environment';
 
 @Component({
   selector: 'cvc-viewer-button',
@@ -18,12 +19,19 @@ export class CvcViewerButtonComponent {
 
   constructor(private queryService: ViewerService, private unreadCountGql: ViewerNotificationCountGQL) {
     this.viewer$ = this.queryService.viewer$;
-    // this.unreadCount$ = this.unreadCountGql.watch(undefined, {pollInterval: 3000})
-    this.unreadCount$ = this.unreadCountGql.watch(undefined)
-      .valueChanges.pipe(
-        map(({data}) => data.notifications.unreadCount),
-        startWith(0)
-      )
+    if(environment.production) {
+      this.unreadCount$ = this.unreadCountGql.watch(undefined, {pollInterval: 5000})
+        .valueChanges.pipe(
+          map(({data}) => data.notifications.unreadCount),
+          startWith(0)
+        )
+    } else {
+      this.unreadCount$ = this.unreadCountGql.watch(undefined)
+        .valueChanges.pipe(
+          map(({data}) => data.notifications.unreadCount),
+          startWith(0)
+        )
+      }
   }
 
   signOut(): void {

client/src/app/components/source-suggestions/source-suggestions-table/source-suggestions-table.component.html

@@ -150,9 +150,10 @@
           </td>
           <td *ngIf="viewer.signedIn">
             <nz-button-group>
-              <button [disabled]="suggestion.status != status.New" 
+              <!-- <button [disabled]="suggestion.status != status.New"  -->
+              <button [disabled]="true"
                 nz-button nzSize="small" 
-                nz-tooltip nzTooltipTitle="Curate an Evidence Item from this Source Suggestion" >
+                nz-tooltip nzTooltipTitle="(Coming Soon) Curate an Evidence Item from this Source Suggestion" >
                 <i nz-icon nzType="plus"></i>
               </button>
               <button 

client/src/app/forms/assertion-revise/assertion-revise.form.html

@@ -28,7 +28,7 @@
         nzShowIcon></nz-alert>
       <ng-template #successMessage
         nzSize="small">
-        <p>View it on the <a routerLink="../../revisions">Revisions Page</a> or suggest another revision below.</p>
+        <p>View it on the <a routerLink="../../revisions">Revisions Page</a>.</p>
       </ng-template>
     </ng-container>
   </ng-template>

client/src/app/forms/config/types/ensembl-input/ensembl-input.module.ts

@@ -4,6 +4,7 @@ import { ensemblVersionValidator, EnsemblInputType, ensemblInputTypeOption, ense
 import { FormlyModule } from '@ngx-formly/core';
 import { FormsModule, ReactiveFormsModule } from '@angular/forms';
 import { NzInputNumberModule } from 'ng-zorro-antd/input-number';
+import { NzInputModule } from 'ng-zorro-antd/input';
 
 @NgModule({
   declarations: [EnsemblInputType],
@@ -16,7 +17,7 @@ import { NzInputNumberModule } from 'ng-zorro-antd/input-number';
       validators: [ensemblVersionValidator],
       validationMessages: [ensemblVersionValidationMessage]
     }),
-    NzInputNumberModule,
+    NzInputNumberModule
   ]
 })
 export class CvcEnsemblInputTypeModule { }

client/src/app/forms/config/types/ensembl-input/ensembl-input.type.ts

@@ -30,7 +30,7 @@ export const ensemblVersionValidator: ValidatorOption = {
       return null;
     } else {
       let versionNum = +c.value;
-      if (versionNum < 76 || versionNum > 150) {
+      if (versionNum < 75 || versionNum > 150) {
         return { 'ensembl-version': true };
       }
       return null;
@@ -41,7 +41,7 @@ export const ensemblVersionValidator: ValidatorOption = {
 export const ensemblVersionValidationMessage: ValidationMessageOption = {
   name: 'ensembl-version',
   message: (_err: any, field: FormlyFieldConfig): string => {
-    return `${field.formControl?.value} is not a valid version of Ensembl. Must be an number between 76 and the latest version of Ensembl.`;
+    return `${field.formControl?.value} is not a valid version of Ensembl. Must be an number between 75 and the latest version of Ensembl.`;
   }
 }
 

client/src/app/forms/config/types/multi-field/multi-field.type.html

@@ -1,7 +1,6 @@
 <div [ngClass]="{ 'hidden': to.hidden === true }">
   <nz-form-item *ngIf="field.fieldGroup?.length === 0">
-    <nz-form-control [nzValidateStatus]="errorState"
-      [nzErrorTip]="errorTpl">
+    <nz-form-control [nzValidateStatus]="errorState">
       <!--
 
       <button nz-button
@@ -15,10 +14,6 @@
         <i nz-icon nzType="plus"></i>
         {{ to.addText }}
       </nz-tag>
-      <ng-template #errorTpl
-        let-control>
-        <formly-validation-message [field]="field"></formly-validation-message>
-      </ng-template>
     </nz-form-control>
   </nz-form-item>
 

client/src/app/forms/config/types/submit-button/submit-button.type.ts

@@ -1,12 +1,13 @@
-import { Component } from '@angular/core';
+import { ChangeDetectionStrategy, Component } from '@angular/core';
 import { FieldType } from '@ngx-formly/core';
 import { Maybe, Organization } from '@app/generated/civic.apollo';
 import {TypeOption} from "@ngx-formly/core/lib/services/formly.config";
 
 @Component({
   selector: 'cvc-submit-button-type',
   templateUrl: './submit-button.type.html',
-  styleUrls: ['./submit-button.type.less']
+  styleUrls: ['./submit-button.type.less'],
+  changeDetection: ChangeDetectionStrategy.OnPush
 })
 export class SubmitButtonComponent extends FieldType {
   _selectedOrg: Maybe<Organization> = undefined;

client/src/app/forms/config/types/tag-input/tag-input.module.ts

@@ -0,0 +1,22 @@
+import { NgModule } from '@angular/core';
+import { CommonModule } from '@angular/common';
+import { TagInputType, TagInputTypeOption } from './tag-input.type';
+import { ReactiveFormsModule } from '@angular/forms';
+import { FormlyModule } from '@ngx-formly/core';
+import { ReactiveComponentModule } from '@ngrx/component';
+import { NzTagModule } from 'ng-zorro-antd/tag';
+import { NzInputModule } from 'ng-zorro-antd/input';
+
+    // MultiFieldTypeOption,
+@NgModule({
+  declarations: [TagInputType],
+  imports: [
+    CommonModule,
+    ReactiveFormsModule,
+    ReactiveComponentModule,
+    FormlyModule.forChild({ types: [TagInputTypeOption] }),
+    NzTagModule,
+    NzInputModule
+  ]
+})
+export class CvcTagInputTypeModule { }

client/src/app/forms/config/types/tag-input/tag-input.type.html

@@ -0,0 +1,9 @@
+<ng-container *ngIf="!formControl.value; else tagItem">
+  <input nz-input
+    [formControl]="formControl"
+    [formlyAttributes]="field"
+    (keydown.enter)="onEnter($event)"/>
+</ng-container>
+<ng-template #tagItem>
+  <nz-tag>{{formControl.value}}</nz-tag>
+</ng-template>

client/src/app/forms/config/types/tag-input/tag-input.type.ts

@@ -0,0 +1,41 @@
+import {
+  ChangeDetectionStrategy,
+  Component,
+} from '@angular/core';
+import { FormControl } from '@angular/forms';
+import { FieldType } from '@ngx-formly/core';
+import { TypeOption } from "@ngx-formly/core/lib/services/formly.config";
+
+@Component({
+  selector: 'cvc-tag-input-type',
+  templateUrl: './tag-input.type.html',
+  styleUrls: ['./tag-input.type.less'],
+  changeDetection: ChangeDetectionStrategy.OnPush
+})
+export class TagInputType extends FieldType {
+  formControl!: FormControl;
+
+  constructor() {
+    super();
+    this.defaultOptions = {
+      templateOptions: {
+        placeholder: 'Enter value',
+      },
+      modelOptions: {
+        updateOn: 'blur'
+      }
+    };
+  }
+
+  onEnter(e: any): void {
+    const input = e.target as HTMLInputElement;
+    this.formControl.setValue(input.value);
+  }
+
+}
+
+
+export const TagInputTypeOption: TypeOption = {
+  name: 'tag-input',
+  component: TagInputType,
+};

client/src/app/forms/config/types/textarea-base/textarea-base.type.html

@@ -1,4 +1,6 @@
 <textarea nz-input
-  [nzAutosize]="to.autosize"
   [formControl]="formControl"
-  [formlyAttributes]="field"></textarea>
+  [formlyAttributes]="field"
+  [nzAutosize]="to.autosize"
+  [placeholder]="to.placeholder">
+</textarea>

client/src/app/forms/config/utilities/input-formatters/variant-revise.ts

@@ -7,34 +7,54 @@ import {
   ReferenceBuild,
 } from '@app/generated/civic.apollo';
 
-export function toClinvarInput(
-  ids?: string[],
-): ClinvarInput {
-  let na, nf;
-  if (ids && ids.includes('N/A')) {
-    ids = undefined;
-    nf = undefined;
-    na = true;
-  } else if (!ids) {
-    ids = undefined;
-    na = undefined;
-    nf = true;
-  } 
+export enum ClinvarOptions {
+  NotApplicable,
+  NoneFound,
+  Found
+}
+
+export function toClinvarInput( ids: string[], optionValue: ClinvarOptions ): ClinvarInput {
+  let na, nf: Maybe<boolean>;
+  let inputIds: Maybe<string[]>
+
+  if(optionValue == ClinvarOptions.Found) {
+    na = undefined
+    nf = undefined
+    inputIds = ids
+  } else if (optionValue == ClinvarOptions.NoneFound) {
+    nf = true
+    na = undefined
+    inputIds = undefined
+  } else {
+    na = true
+    nf = undefined
+    inputIds = undefined
+  }
 
-  return <ClinvarInput>{
-    ids: ids ? ids.map(id => +id) : undefined,
+  return {
+    ids: inputIds ? inputIds.map(id => +id) : undefined,
     noneFound: nf,
     notApplicable: na
   };
 }
 
-export function toCoordinateInput(coord: Coordinate): CoordinateInput {
-  return <CoordinateInput>{
-    chromosome: undefinedIfEmpty(coord.chromosome),
-    representativeTranscript: undefinedIfEmpty(coord.representativeTranscript),
-    start: coord.start ? +coord.start: undefined,
-    stop: coord.stop ? +coord.stop: undefined,
-  };
+export function toCoordinateInput(coord: Maybe<Coordinate>): CoordinateInput {
+  if (coord) {
+    return {
+      chromosome: undefinedIfEmpty(coord.chromosome),
+      representativeTranscript: undefinedIfEmpty(coord.representativeTranscript),
+      start: coord.start ? +coord.start: undefined,
+      stop: coord.stop ? +coord.stop: undefined,
+    };
+  }
+  else {
+    return {
+      chromosome: undefined,
+      representativeTranscript: undefined,
+      start: undefined,
+      stop: undefined,
+    }
+  }
 }
 
 export function toNullableReferenceBuildInput(
@@ -83,4 +103,4 @@ export const Chromosomes = [
   {value: 'X', label:  'X'},
   {value: 'Y',  label:  'Y'},
   {value: 'MT',  label:  'MT'}
-];
+];

client/src/app/forms/config/validators/default.validators.ts

@@ -43,18 +43,52 @@ export const defaultMessages: ValidationMessageOption[] = [
       return `Value must be an integer.`;
     }
   },
-
+  {
+    name: 'nucleotide',
+    message: (_err: any, ffc: FormlyFieldConfig): string => {
+      return `Value must only contain A, C, T, G, and/or /.`;
+    }
+  },
+  {
+    name: 'clinvar',
+    message: (_err: any, ffc: FormlyFieldConfig): string => {
+      return `Value must be an integer.`;
+    }
+  }
 ];
 
 export const defaultValidators: ValidatorOption[] = [
   {
     name: 'integer',
     validation: (fc: AbstractControl, ffc: FormlyFieldConfig): ValidationErrors | null => {
-      if (fc.value === '' || fc.value === undefined) {
+      if (fc.value === '' || fc.value === undefined || fc.value === null) {
         return null;
       } else {
         return /^\d+$/.test(fc.value) ? null : { 'integer': true }
       }
     },
   },
+  {
+    name: 'nucleotide',
+    validation: (fc: AbstractControl, ffc: FormlyFieldConfig): ValidationErrors | null => {
+      if (fc.value === '' || fc.value === undefined || fc.value === null) {
+        return null;
+      } else {
+        return /^[ACTG\/]+$/.test(fc.value) ? null : { 'nucleotide': true }
+      }
+    }
+  },
+  {
+    name: 'clinvar',
+    validation: (fc: AbstractControl, ffc: FormlyFieldConfig): ValidationErrors | null => {
+      for (var value of fc.value) {
+        if (!(value === '' || value === undefined || value === null)) {
+          if ( !(/^\d+$/.test(value)) ) {
+            return {'clinvar': true}
+          }
+        }
+      }
+      return null
+    }
+  }
 ];